Simulation in Chemistry and Biochemistry

3 units

This course explores a wide range molecular modeling techniques and applications of computational chemistry to problems in chemistry and biochemistry. Topics include ab initio quantum mechanics, semi-empirical MO theory, molecular mechanics, molecular dynamics simulation, coarse-grained models, electrostatic methods and biomolecular structure prediction. A major component of the course is weekly laboratory sessions using common software programs in the field, including Spartan, Q-Chem, Gaussian, VMD, TINKER, APBS, AutoDock, SDA7 and others. Many of the lab exercises target proteins, nucleic acids and other biological structures. As a final lab experience, students will complete an independent project using tools covered in the course.